Upgrade of Abisko's operating system from Ubuntu Lucid to Ubuntu Precise

Upgrade of Abisko's operating system

We are going to upgrade Abisko from Ubuntu 10.04 (Lucid) to Ubuntu 12.04 (Precise) during November. 
The upgrade to Precise includes upgrades to a lot of the system software. Of interest to you, as a user, are mainly the GNU compiler (which will be upgraded to version 4.6), and Python (which will be upgraded to version 2.7).
Due to this upgrade we have also removed some older versions of software we had installed, to reduce our maintenance load, and upgraded and/or recompiled some existing software and libraries. We therefor strongly recommend that you recompile anything you have installed yourself, both to make sure it actually works on the upgraded system, and to take advantage of upgraded libraries and compilers.
We have prepared a new login node with the environment we are going to end up with. We strongly advise you to login to that node to verify that the software you are using works. There is also a small partition to test things out on, with a very limited runtime, 30 minutes, which should be enough to make sure your old or new binaries can run.

Our normal build instructions are still valid, although module versions may have changed.

Make sure to check your submit files and verify that they are valid for the modules used.

We have made (almost) all currently existing software modules available on the upgraded system, either as simple copies of the current builds or as recompiled versions when needed due to changes in modules they depend on.
We have done rudimentary testing of all packages we have pre-installed (as modules), but we can of course not test every aspect of every code. Therefore, if you find anything that doesn't work, please let us know immediately by sending a mail to support@hpc2n.umu.se stating which code it is, and that it is on the Precise test system.
During the upgrade, we will rebuild almost everything with better optimisation and possibly install newer versions if they exist.

What about support for the current Lucid system?

We will as of now basically stop support for anything installed on the Lucid system. All our efforts need to be directed at the new Precise system.

How is the migration done?

On 2013-11-22 we will stop submissions to the old Lucid system. At that time we will have expanded the Precise part of the batch system so it will be able to handle a production load.
When submission to the Lucid system is stopped we will reinstall the old login node and the temporary login node will be removed.

The Lucid part will then be run for 6 days allowing as many as possible of the existing old jobs to finish. After that nodes will be migrated as needed to keep up with the increased load of the Precise system.

After another 7 days we will stop the Lucid part of the system and any jobs still in the Lucid part of the queue will be deleted since they will fail to run if transferred to the Precise part.

During the migration there is a slight risk of unforseen problems that may force us to reinstall compute nodes and/or the login node, or otherwise make larger changes, thereby causing interruptions in your work. We will however strive to make such work as smooth and quick as possible.

In the unlikely event of serious problems, (showstoppers), the upgrade will be suspended until such problems are fixed.

Updates on how the migration is progressing, any problems etc, will be posted on our System News.

Testing on the Precise login node: 

The new login node is named abisko-precise (abisko-precise.hpc2n.umu.se).
From this login node the Precise part of the batch system is the default partition used, and you will by default only see this part when looking at the queue.
The partition consist of 4 nodes, for a total of 192 cores.

Important changes to the batch system

We are no longer allowing the use of --mem-per-cpu. If you need more than the default amount of memory per cpu (core) (2500MB), you need to allocate more cores to your job using --cpus-per-task (-c). You can then use those cores if your code allows it.

What has actually been upgraded?

A short list of software that has been upgraded (with the operating system or by us) is available. That list will be updated with new information if and when packages have been upgraded.

Updated: 2018-03-21, 17:35